You should be able to shoot through glass just by using a polarizing filter on the lens. I have done it many times. (Copy work is, in fact, my only use for polarizing filters.) Place the lights at identical angles and distances to the original. 45 degrees is standard, but this need not be adhered to. All you need is light that sculpts the artwork in the desired manner, but which provides the same amount of illumination to all dimensions of the piece. In other words, an incident meter should read the same no matter where you place it over the piece. Even if not using a 1:1 ratio, for a more sculpted effect, light evens out across the surface if you move it back from the subject.
If you are still having trouble, try fine grids (10 degree or narrower square or honeycomb pattern) instead of polarizing gels. The shape of the reflectors of the lamps should ideally be rectangular, but this is rarely the case on copy stand. Most have round reflectors. Backing the lamps off will eliminate hot spots that may form with the grids on. Ideally you use free-standing big rectangular lamps instead of those tiny round ones that mount to the stand. I do all my copy work on a wall or sometimes a table with Mole-Richardson 1000W Super Softlites. They provide a large reflected (read even) light, which I modify more by using the stock M-R grids for these lamps. Glass or not, I use a polarizing filter unless the surface is dead matte.
3D objects are a different story. You need reflections to make them look realistic (i.e. not 2 dimensional).
FWIW, I use my SINAR with the Rodenstock 210 or 90 lenses, often with a roll film back, and Ilford Ortho in HC-110 for continuous tone or Rollei ATP 1.1 in D-19 for halftone.